Functionalized silicon surfaces constitute an area of intense scientific interest. Our theoretical work in this exciting area can be broadly divided into two categories; the first is calculating the spectra of functionalized silicon surfaces to understand surface structure and the second is calculating the chemistry of funtionalization of the silicon surface with the surface as a reagent. Using electronic structure theory we have investigated the relationship between the molecular vibrations of cluster and periodic models for the functionalized Si(111) surface. From this work, we have developed a technique for calculating periodic vibrational frequencies using small cluster models. In addition, we have used the method to explain the coupling of near-surface phonon modes with adsorbate vibrational frequencies seen in experimental spectra. The method has been shown to be robust for uniform and mixed coverage (halide/hydrogen) surfaces. A careful study of the silicon hydrogen modes for many reconstructions at the same level of theory has been carried out to understand the spectra of hydrogen-passivated silicon surfaces. For the Si(100) surface we have examined the radical-initiated chain reactions of allylic mercaptan that have the unique property of growing exclusively across dimer rows on the Si(100) surface. We discuss the mechanisms of Lewis acids degrading on the silicon surface and the hydrogen induced insertion of oxygen or nitrogen into the silicon surface.